A. Elcock

发表

Prediction of functionally important residues based solely on the computed energetics of protein structure.

A. Elcock, 2001, Journal of molecular biology.

Rapid computational identification of the targets of protein kinase inhibitors.

A. Elcock, W. M. Rockey, 2005, Journal of medicinal chemistry.

Computing ionization states of proteins with a detailed charge model

M. Gilson, A. Elcock, J. Briggs, 1996, J. Comput. Chem..

Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase.

Adrian H Elcock, A. Elcock, Tamara Frembgen-Kesner, 2006, Journal of molecular biology.

Physicochemical Properties of Cells and Their Effects on Intrinsically Disordered Proteins (IDPs)

L. Gierasch, A. Elcock, Conggang Li, 2014, Chemical reviews.

Identification of protein oligomerization states by analysis of interface conservation

A. Elcock, J. Mccammon, J. McCammon, 2001, Proceedings of the National Academy of Sciences of the United States of America.

The stability of salt bridges at high temperatures: implications for hyperthermophilic proteins.

A. Elcock, 1998, Journal of molecular biology.

Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other.

A. Elcock, Casey T. Andrews, 2013, Journal of chemical theory and computation.

Electrostatic contributions to the stability of halophilic proteins.

J A McCammon, A H Elcock, A. Elcock, 1998, Journal of molecular biology.

The C-terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility

A. Elcock, K. T. Powers, M. Washington, 2018, Nucleic acids research.

Atomic-level observation of macromolecular crowding effects: Escape of a protein from the GroEL cage

Adrian H Elcock, A. Elcock, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Structure selection for protein kinase docking and virtual screening: homology models or crystal structures?

Adrian H Elcock, William M Rockey, A. Elcock, 2006, Current protein & peptide science.

Molecular Behavior in Biological Cells The Bacterial Cytoplasm as a Model System

A. Elcock, A. S. Thomas, 2011 .

Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins.

A. Elcock, Tamara Frembgen-Kesner, 2009, Journal of chemical theory and computation.

Computer Simulation of Protein−Protein Interactions

A. Elcock, J. Mccammon, David S. Toledano and, 2001 .

Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association.

A. Elcock, Tamara Frembgen-Kesner, 2010, Biophysical journal.

The Native 3D Organization of Bacterial Polysomes

Julio O. Ortiz, A. Elcock, W. Baumeister, 2009, Cell.

Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations.

A. Elcock, Casey T. Andrews, Brady A Campbell, 2017, Journal of chemical theory and computation.

Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements.

Wesley K. Lay, A. Elcock, M. S. Miller, 2016, Journal of chemical theory and computation.

Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics Simulations.

A. Elcock, Casey T. Andrews, Michael V. Schrodt, 2015, Journal of chemical theory and computation.

COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids

A. Elcock, Casey T. Andrews, 2014, Journal of chemical theory and computation.

Correction to Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics Simulations.

A. Elcock, Casey T. Andrews, Michael V. Schrodt, 2018, Journal of chemical theory and computation.

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

Adrian H Elcock, A. Elcock, Tamara Frembgen-Kesner, 2015, Journal of chemical theory and computation.

Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome

Adrian H. Elcock, A. Elcock, Shuxiang Li, 2017, Nucleic acids research.

A PEG‐Based Oligomer as a Backbone Replacement for Surface‐Exposed Loops in a Protein Tertiary Structure

A. Elcock, W. S. Horne, Z. E. Reinert, 2012, Chembiochem : a European journal of chemical biology.

Models of macromolecular crowding effects and the need for quantitative comparisons with experiment.

Adrian H Elcock, A. Elcock, 2010, Current opinion in structural biology.

Sequence selective binding to the DNA major groove: tris(1,10-phenanthroline) metal complexes binding to poly(dG-dC) and poly(dA-dT).

A. Elcock, I. Haworth, J. Freeman, 1991, Journal of biomolecular structure & dynamics.

p38α Mitogen-Activated Protein Kinase Is a Druggable Target in Pancreatic Adenocarcinoma

A. Elcock, Shun Zhu, J. Zuo, 2019, Front. Oncol..

COMBINED QUANTUM AND MOLECULAR MECHANICAL STUDY OF DNA CROSS-LINKING BY NITROUS ACID

A. Elcock, P. Lyne, A. Mulholland, 1995 .

Atomically detailed simulations of concentrated protein solutions: the effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems.

Adrian H Elcock, A. Elcock, S. McGuffee, 2006, Journal of the American Chemical Society.

Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field.

A. Elcock, Casey T. Andrews, Austin C Stark, 2013, Journal of chemical theory and computation.

A molecule-centered method for accelerating the calculation of hydrodynamic interactions in Brownian dynamics simulations containing many flexible biomolecules.

A. Elcock, 2013, Journal of chemical theory and computation.

Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study.

A. Elcock, Shun Zhu, S. M. Travis, 2013, Journal of chemical theory and computation.

Direct observation of salt effects on molecular interactions through explicit-solvent molecular dynamics simulations: differential effects on electrostatic and hydrophobic interactions and comparisons to Poisson-Boltzmann theory.

A. Elcock, A. S. Thomas, 2006, Journal of the American Chemical Society.

Molecular Simulations of Diffusion and Association in Multimacromolecular Systems

Adrian H Elcock, A. Elcock, 2004, Numerical Computer Methods, Part D.

Mathematics and Molecular Neurobiology

Nathan A. Baker, Richard H. Henchman, A. Elcock, 2002 .

Molecular Modeling of the Bacterial Cytoplasm

A. Elcock, 2010 .

Computer simulations of the bacterial cytoplasm

Adrian H. Elcock, A. Elcock, Tamara Frembgen-Kesner, 2013, Biophysical Reviews.

Dynamic binding of replication protein a is required for DNA repair

A. Elcock, M. Spies, M. Wold, 2016, Nucleic acids research.

A Complete Thermodynamic Characterization of Electrostatic and Hydrophobic Associations in the Temperature Range 0 to 100 °C from Explicit-Solvent Molecular Dynamics Simulations

A. Elcock, Shun Zhu, 2010 .

Sequence Dependent Hydration of DNA: Theoretical Results

A. Elcock, J. Mccammon, 1995 .

Reparameterization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations

Wesley K. Lay, A. Elcock, M. S. Miller, 2017 .

Design principles that protect the proteasome from self‐destruction

A. Elcock, A. Matouschek, A. K. Singh Gautam, 2020, Protein science : a publication of the Protein Society.

Computer simulations of the bacterial cytoplasm

A. Elcock, Tamara Frembgen-Kesner, 2013, Biophysical Reviews.

Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient.

J A McCammon, A H Elcock, A. Elcock, 2001, Biophysical journal.

Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment.

A. Elcock, Casey T. Andrews, Reid F Brown, 2015, Journal of chemical theory and computation.

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

Adrian H. Elcock, Sean R. McGuffee, A. Elcock, 2010, PLoS Comput. Biol..

Human Heterochromatin Protein 1α Promotes Nucleosome Associations That Drive Chromatin Condensation*

A. Elcock, L. Wallrath, C. Woodcock, 2014, The Journal of Biological Chemistry.

Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations.

Wesley K. Lay, A. Elcock, M. S. Miller, 2017, Journal of chemical theory and computation.

Mechanism of action of antifreeze polypeptide HPLC6 in solution: analysis of solvent behaviour by molecular dynamics

W. Richards, A. Elcock, G. Grant, 1996 .

Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome

A. Elcock, 2006, PLoS Comput. Biol..

Modeling supramolecular assemblages.

Adrian H Elcock, A. Elcock, 2002, Current opinion in structural biology.

Molecular chaperones: providing a safe place to weather a midlife protein-folding crisis

A. Elcock, P. Clark, 2016, Nature Structural &Molecular Biology.

Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind's AlphaFold2 Program Dramatically Expands the Metalloproteome.

A. Elcock, Zachary J. Wehrspan, Robert T. McDonnell, 2021, Journal of molecular biology.

Cotranslational assembly imposes evolutionary constraints on homomeric proteins

S. Teichmann, M. Babu, N. Sugimoto, 2016, bioRxiv.

Flexibility of the bacterial chaperone trigger factor in microsecond-timescale molecular dynamics simulations.

A. Elcock, A. S. Thomas, Suifang Mao, 2013, Biophysical journal.

The pH dependence of stability of the activation helix and the catalytic site of GART.

A. Elcock, J. Mccammon, P. Jennings, 2003, Biophysical chemistry.

Proton transfer dynamics of GART: The pH‐dependent catalytic mechanism examined by electrostatic calculations

A. Elcock, J. Mccammon, P. Jennings, 2001, Protein science : a publication of the Protein Society.

Native‐state conformational dynamics of GART: A regulatory pH‐dependent coil–helix transition examined by electrostatic calculations

A. Elcock, J. Mccammon, P. Jennings, 2001, Protein science : a publication of the Protein Society.

Dynamics and Energy Contributions for Transport of Unfolded Pertactin through a Protein Nanopore.

A. Elcock, P. Clark, J. Pelta, 2015, ACS nano.

Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge.

P Taylor, J A McCammon, J M Briggs, 1998, Biopolymers.

Electrostatic channeling of substrates between enzyme active sites: comparison of simulation and experiment.

A. Elcock, J. Mccammon, G. Huber, 1997, Biochemistry.

Application of Poisson—Boltzmann solvation forces to macromolecular simulations

J. Andrew McCammon, Adrian H. Elcock, A. Elcock, 1997 .

Atomistic simulations of competition between substrates binding to an enzyme.

A. Elcock, 2002, Biophysical journal.

Evidence for electrostatic channeling in a fusion protein of malate dehydrogenase and citrate synthase.

J A McCammon, A H Elcock, A. Elcock, 1996, Biochemistry.

Electrostatic channeling in the bifunctional enzyme dihydrofolate reductase-thymidylate synthase.

D. Knighton, A. Elcock, J. Mccammon, 1996, Journal of molecular biology.

ATP and AMP Mutually Influence Their Interaction with the ATP-binding Cassette (ABC) Adenylate Kinase Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) at Separate Binding Sites*

A. Elcock, M. Welsh, Qian Dong, 2013, The Journal of Biological Chemistry.

Identification of Iron-Sulfur (Fe-S) and Zn-binding Sites Within Proteomes Predicted by DeepMind’s AlphaFold2 Program Dramatically Expands the Metalloproteome

A. Elcock, Zachary J. Wehrspan, Robert T. McDonnell, 2021, bioRxiv.

Reparameterization of Solute-Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations.

Wesley K. Lay, A. Elcock, M. S. Miller, 2017, Journal of chemical theory and computation.

Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization.

Wesley K. Lay, A. Elcock, M. S. Miller, 2016, The journal of physical chemistry. B.

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

S. Teichmann, M. Babu, N. Sugimoto, 2018, Nature Structural & Molecular Biology.

Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry.

J A McCammon, A H Elcock, A. Elcock, 1999, Journal of molecular biology.

Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin.

J A McCammon, R C Wade, A H Elcock, 1999, Journal of molecular biology.

Theoretical studies of the intercalation of 9-hydroxyellipticine in DNA.

W. Richards, A. Elcock, A. Rodger, 1998, Biopolymers.

Molecular Dynamics Simulations Predict a Favorable and Unique Mode of Interaction between Lithium (Li(+)) Ions and Hydrophobic Molecules in Aqueous Solution.

A. Elcock, A. S. Thomas, 2011, Journal of chemical theory and computation.

An Orientationally Averaged Version of the Rotne-Prager-Yamakawa Tensor Provides A Fast But Still Accurate Treatment Of Hydrodynamic Interactions In Brownian Dynamics Simulations Of Biological Macromolecules

A. Elcock, John Tworek, 2023, bioRxiv.

AutoRNC: an automated modeling program for building atomic models of ribosome-nascent chain complexes

A. Elcock, Robert T. McDonnell, 2023, bioRxiv.

Molecular dynamics simulations of hydrophobic associations in aqueous salt solutions indicate a connection between water hydrogen bonding and the Hofmeister effect.

A. Elcock, A. S. Thomas, 2007, Journal of the American Chemical Society.

Multi-scale Modeling and Experimental Data Enable Structural Models of the Escherichia Coli Peptidoglycan to be Constructed on the Whole-Cell Scale

A. Elcock, Zachary J. Wehrspan, 2023, bioRxiv.

Atomic Models of All Major Trans-Envelope Complexes Involved in Lipid Trafficking in Escherichia Coli Constructed Using a Combination of AlphaFold2, AF2Complex, and Membrane Morphing Simulations

A. Elcock, Zachary J. Wehrspan, Robert T. McDonnell, 2023, bioRxiv.

Electrostatic effects in homeodomain-DNA interactions.

J A McCammon, J M Briggs, A H Elcock, 1997, Journal of molecular biology.

Relative hydration free energies of nucleic acid bases

W. Richards, A. Elcock, 1993 .

Modeling the 3D structure and conformational dynamics of very large RNAs using coarse-grained molecular simulations

A. Elcock, Robert T. McDonnell, Aaron N. Henderson, 2023, bioRxiv.

Easy Removal of Steric Clashes and Entanglements in Macromolecular Systems by Temporary Addition of a Fourth Spatial Dimension

A. Elcock, 2023, bioRxiv.

spotter: A single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes

A. Elcock, William C. Hacker, 2023, bioRxiv.

Direct Measurement of the Kinetics and Thermodynamics of Association of Hydrophobic Molecules from Molecular Dynamics Simulations.

A. Elcock, A. S. Thomas, 2011, The journal of physical chemistry letters.

spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.

A. Elcock, William C. Hacker, 2023, Nucleic acids research.

Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins.

A. Elcock, Shuxiang Li, 2015, The journal of physical chemistry letters.

Orientationally Averaged Version of the Rotne–Prager–Yamakawa Tensor Provides a Fast but Still Accurate Treatment of Hydrodynamic Interactions in Brownian Dynamics Simulations of Biological Macromolecules

A. Elcock, John Tworek, 2023, Journal of chemical theory and computation.

A. Elcock, Tamara Frembgen-Kesner, Casey T. Andrews, 2015, Journal of chemical theory and computation.

Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other.

A. Elcock, Casey T. Andrews, 2013, Journal of chemical theory and computation.

Molecular simulations suggest protein salt bridges are uniquely suited to life at high temperatures.

A. Elcock, A. S. Thomas, 2004, Journal of the American Chemical Society.

Realistic modeling of the denatured states of proteins allows accurate calculations of the pH dependence of protein stability.

A. Elcock, 1999, Journal of molecular biology.

A PEG‐Based Oligomer as a Backbone Replacement for Surface‐Exposed Loops in a Protein Tertiary Structure

A. Elcock, Z. E. Reinert, Eli D Musselman, 2012, ChemBioChem.